Lopetegui was stunningly sacked as Spain coach, just a day before the beginning of the World Cup.
It came just a day after it was revealed Lopetegui was taking over as Real Madrid boss, news Rubiales says he only found out minutes before the announcement.
Amid reports the players had pleaded for Lopetegui to remain in charge, Rubiales insisted the squad were happy ahead of the showpiece tournament.
"I have listened to everyone, but the decision is mine," he said. "The players are completely determined to make a great World Cup. There is no mutiny, the players are doing very well."
Real Madrid great Fernando Hierro will lead Spain – which faces Portugal, Iran and Morocco in Group B – at the World Cup.
Rubiales said the appointment of the 50 year-old had been well received by the players.
"The players have welcomed Hierro and have told me they will be with him to the death, with [Sergio] Ramos very well, acting as captain," he said.
Spain begins its campaign with a clash against Portugal in Sochi.